[2024-01-25 19:34:21,001] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:21,003] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:21,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d163914-4f6c-4cda-9769-fe65a9320d86/dqc_reference
[2024-01-25 19:34:22,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:22,102] [INFO] Task started: Prodigal
[2024-01-25 19:34:22,103] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8cfb4e0-78f5-43db-a80f-f24822a15bff/GCF_000337015.1_ASM33701v1_genomic.fna.gz | prodigal -d GCF_000337015.1_ASM33701v1_genomic.fna/cds.fna -a GCF_000337015.1_ASM33701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:34:34,175] [INFO] Task succeeded: Prodigal
[2024-01-25 19:34:34,175] [INFO] Task started: HMMsearch
[2024-01-25 19:34:34,175] [INFO] Running command: hmmsearch --tblout GCF_000337015.1_ASM33701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d163914-4f6c-4cda-9769-fe65a9320d86/dqc_reference/reference_markers.hmm GCF_000337015.1_ASM33701v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:34:34,399] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:34:34,400] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf8cfb4e0-78f5-43db-a80f-f24822a15bff/GCF_000337015.1_ASM33701v1_genomic.fna.gz]
[2024-01-25 19:34:34,427] [INFO] Query marker FASTA was written to GCF_000337015.1_ASM33701v1_genomic.fna/markers.fasta
[2024-01-25 19:34:34,428] [INFO] Task started: Blastn
[2024-01-25 19:34:34,428] [INFO] Running command: blastn -query GCF_000337015.1_ASM33701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d163914-4f6c-4cda-9769-fe65a9320d86/dqc_reference/reference_markers.fasta -out GCF_000337015.1_ASM33701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:34,918] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:34,921] [INFO] Selected 6 target genomes.
[2024-01-25 19:34:34,921] [INFO] Target genome list was writen to GCF_000337015.1_ASM33701v1_genomic.fna/target_genomes.txt
[2024-01-25 19:34:34,923] [INFO] Task started: fastANI
[2024-01-25 19:34:34,924] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8cfb4e0-78f5-43db-a80f-f24822a15bff/GCF_000337015.1_ASM33701v1_genomic.fna.gz --refList GCF_000337015.1_ASM33701v1_genomic.fna/target_genomes.txt --output GCF_000337015.1_ASM33701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:41,914] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:41,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d163914-4f6c-4cda-9769-fe65a9320d86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:41,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d163914-4f6c-4cda-9769-fe65a9320d86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:41,920] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:34:41,921] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:34:41,921] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Halorubrum arcis	strain=JCM 13916	GCA_000337015.1	368454	368454	type	True	100.0	1078	1080	95	inconclusive
Halorubrum distributum	strain=JCM 9100	GCA_000337055.1	29283	29283	suspected-type	True	97.8133	874	1080	95	inconclusive
Halorubrum distributum	strain=JCM 10118	GCA_000337335.1	29283	29283	suspected-type	True	97.771	892	1080	95	inconclusive
Halorubrum ezzemoulense	strain=DSM 17463	GCA_000421805.1	337243	337243	type	True	89.7623	818	1080	95	below_threshold
Halorubrum coriense	strain=DSM 10284	GCA_000337035.1	64713	64713	type	True	89.6953	781	1080	95	below_threshold
Halorubrum ezzemoulense	strain=DSM 17463	GCA_002114285.1	337243	337243	type	True	89.6697	787	1080	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:34:41,922] [INFO] DFAST Taxonomy check result was written to GCF_000337015.1_ASM33701v1_genomic.fna/tc_result.tsv
[2024-01-25 19:34:41,923] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:41,923] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:41,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d163914-4f6c-4cda-9769-fe65a9320d86/dqc_reference/checkm_data
[2024-01-25 19:34:41,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:41,959] [INFO] Task started: CheckM
[2024-01-25 19:34:41,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337015.1_ASM33701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337015.1_ASM33701v1_genomic.fna/checkm_input GCF_000337015.1_ASM33701v1_genomic.fna/checkm_result
[2024-01-25 19:35:16,398] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:16,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:16,420] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:16,420] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:16,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337015.1_ASM33701v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:16,421] [INFO] Task started: Blastn
[2024-01-25 19:35:16,422] [INFO] Running command: blastn -query GCF_000337015.1_ASM33701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d163914-4f6c-4cda-9769-fe65a9320d86/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337015.1_ASM33701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:16,931] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:16,934] [INFO] Selected 8 target genomes.
[2024-01-25 19:35:16,935] [INFO] Target genome list was writen to GCF_000337015.1_ASM33701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:16,939] [INFO] Task started: fastANI
[2024-01-25 19:35:16,939] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8cfb4e0-78f5-43db-a80f-f24822a15bff/GCF_000337015.1_ASM33701v1_genomic.fna.gz --refList GCF_000337015.1_ASM33701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337015.1_ASM33701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:27,293] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:27,299] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:27,299] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000337335.1	s__Halorubrum distributum	97.7971	891	1080	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.52	97.80	0.88	0.83	7	conclusive
GCF_018228765.1	s__Halorubrum sp000296615	93.2012	838	1080	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.09	99.09	0.95	0.95	2	-
GCF_003666015.1	s__Halorubrum sp003666015	92.8716	860	1080	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355655.1	s__Halorubrum trapanicum_A	92.5245	825	1080	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102375.1	s__Halorubrum xinjiangense	91.3338	826	1080	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336875.1	s__Halorubrum californiense	91.0068	783	1080	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.69	99.69	0.88	0.88	2	-
GCF_001280455.1	s__Halorubrum tropicale	90.4976	830	1080	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	97.18	95.21	0.82	0.77	8	-
GCF_017873555.1	s__Halorubrum trapanicum	90.4199	776	1080	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:27,300] [INFO] GTDB search result was written to GCF_000337015.1_ASM33701v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:27,302] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:27,304] [INFO] DFAST_QC result json was written to GCF_000337015.1_ASM33701v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:27,304] [INFO] DFAST_QC completed!
[2024-01-25 19:35:27,304] [INFO] Total running time: 0h1m6s